Microbiome: Health is All About the Bugs Within You

by | Jun 6, 2018 | Gut Health, Lupus Blog | 0 comments

Hi, Dr. Connie here.

Over this past weekend, I enjoyed a jam packed few days, rubbing shoulders with the big names in Functional Medicine, including Dr. Amy Myers, Dr. Mark Hyman, Dr. Steven Gundry, Dr. Terry Wahls, and my favorite, Dr. Alessio Fasano.

I attended the Annual International Conference lead by the Institute of Functional Medicine. This year’s topic was autoimmune disease.

I met lots of like minded practitioners from all over the world and it was truly a worth while experience.

I will be sharing what I learned over the coming weeks, but today I want to start with the most pertinent information regarding our microbiome as it relates to inflammation, leading to all chronic diseases.

What is Microbiome?

Microbiome is a hot topic in the field of Functional and Integrative Medicine.

Microbiome refers to the microorganisms in our body.  We depend on a vast army of microbes to stay alive. A microbiome not only protects us against infections and germs, but it is also responsible for our metabolism.

It helps to break down food, release energy, and make bioavailable vitamins for our cells to use for optimal function.

The problem is that often, we have what’s referred to as dysbiosis.  Dysbiosis refers to an imbalance of health promoting bacteria and disease causing bacteria.

This in turn causes nutrient deficiency, leaky gut, and immune dysregulation, leading to inflammation which ultimately causes disease.

The root of any chronic disease is inflammation.  The most common symptoms that most struggle with are obesity, brain fog, high blood pressure, insulin resistance, GERD, and pain.

Confusion and Chaos

With growing number of authors writing nutrition and diet books, it’s becoming harder to understand exactly what our diet should consist of.

There were three experts at the roundtable discussion promoting their new books, one promoting the specifics of plant based diet and another promoting the paleo-mediterranean diet, while the last one argued that food really isn’t the enemy.

Then there were a plethora of exhibitors promoting various supplements, keto plans, laboratory testing, and herbals.  All this excitement used to be fun for me 10 years ago when I first got introduced to Functional Medicine.

However, as a patient who’s applying the concepts to my own life, it can still be confusing and overwhelming even for me.

As a Lupus patient and a clinician obsessed with progressive cutting edge information, everything that was said over the weekend was nothing new.

What Diet is the Right Diet?

With the media going crazy over keto diets, one presenter shared the detriment of such a diet for an obese Rheumatoid patient named Jane.

She went on a keto diet which eliminated carbs and incorporated lots of healthy fats and healthy vegetables and fruits.

After about 6 months on this diet, Jane lost 40 lbs but she began to have swelling and achy joints with her laboratory markers clearly out of normal range, indicating positive inflammatory markers.

For Jane, the keto diet worked to lose weight short term, but due to her microbiome composition, it ended up causing more inflammation in her body.

This was due to her genetic predisposition, coupled with her dysbiosis wrecking havoc in her metabolism in such a way to lose lean muscle tissue rather than losing her fat.

What we are now learning is that a very low carb diet is more effective than a low fat diet for short term weight loss.

On a keto diet, you may lose weight, but are you losing fat?  Based on a study, body fat loss slowed during the keto diet and loss of lean muscle increased. (1)

Focus on the BUGS

What’s important is not to focus on the type of diet, but focus on the microbiome.

For example, patients with autoimmune disease exhibited decreased bacterial diversity compared with controls. (2)

Also a diet high in saturated fats lead to decreased gut bacterial diversity.  Saturated fats include fats from animal foods like beef, lamb, pork, chicken with skin, whole milk, cheese, etc.

Rather than getting lost in what type of diet we should follow, we need to address the underlying biology of multiple components of the systems as a whole.

What does this mean for you?  Thinking about the whole picture rather than thinking of the sum of the parts because after all, we are a whole being.

Truth is that we are 99% bacteria and 1 % human.

The role of our microbiome (collective bacteria in our gut) plays a huge role in our immunity and inflammation.

What we know is that all disease begins with inflammation and autoimmunity is prevalent in all of us.

Our microbiome plays a major role by “modulating” a balanced immune response.

The disruption of our microbiome by intake of modern drugs and lifestyle plays a huge role in autoimmune and inflammatory diseases. (2)

We can no longer ignore the role that our intestinal microbial bacteria plays in modulating our immune system and ultimately our overall health.

Microbiome determines the effectiveness of the nutrients that we consume.  It affects how we metabolize our food and the composition and the function of the microbiome can predict the effectiveness of dietary changes.

Not only do we need to know the good bacteria from the bad, but we need to know specifically who lives within us.  Knowing specific bacterial species will determine how to balance our gut.

This is because there are significant immunological and metabolic properties of each bacteria.  The effect can be both health promoting or disease promoting.

When we refer to leaky gut, we know there are holes to invite the bad into our body.  We want tight junctions to keep the bad out and absorb the good.

Now we know that certain bacterial strains increase tight junctions but they vary depending on the type of bacterial strain.

Role of Virus in the Human Microbiome

Viruses are commonly found in our microbiome.  They are readily absorbed through our gut barrier and their effects are not very well understood.

We do now understand that viral infection and antiviral immunity contribute to the development of autoimmunity.  (3)

Importance of Butyrate

Butyrate is a type of fatty acid that helps our gut function.  It’s especially important for those with autoimmunity.  (4)

Butyrate is present when our gut microbiome reacts with fiber that we consume, causing “fermentation”.  For some of us who have yeast or bacterial imbalance, we may have signs and symptoms of gas and bloating.

Butyrate is produced when our gut ferments certain types of fiber.  Our gut needs butyrate to function properly because it helps the health of our gut by making sure that there’s a healthy balance of new and old cells.

Butyrate is important and helps with the following:

  • Intestinal health
  • Immune balance/anti-inflammation
  • Suppression of cancer cells
  • Brain health and longevity
  • Weight control
  • Insulin sensitivity
  • Dietary balance
  • Microbiome balance

So How Do We Increase Butyrate?

  1. Add bacteria from foods or supplements (probiotics)
  2. Feed the bacteria (prebiotics, vegetables)

But if you’ve been given antibiotics, then we’ve got another layer of problems to solve.

We need to supply good probiotics and then eat prebiotics to nourish the gut bacteria so that the good guys can prosper and the bad guys don’t have a chance.

Autoimmunity and Butyrate

For autoimmune patients, there’s lower butyrate production compared to an average person.  As we mentioned, lower levels of butyrate increase inflammation and result in joint and muscle pain.

Lower levels can be also caused by our autoimmune condition as well as antibiotic use.


So to recap today’s message.

Our microbiome determines the metabolic function of our body.

It’s important to know who lives within us to understand how to support our health.

We are all different, so we need an individualized approach to food rather than following a general diet such as keto.

Our microbiome plays a key role in modulating our immune system.

Butyrate is necessary to provide a protective barrier in our gut.

Eating healthy fiber from certain vegetables and fruits can promote healthy butyrate production.

Butyrate can also have an immune modulating effect

We need to do everything we can to follow an anti-inflammatory living plan.

Here at Alkaline Wellness believe in bioindividuality.  We don’t believe in a specific diet for everyone, rather, we believe in first starting with YOU and then figuring out the right food plan specific to your needs based on your health history and current symptoms or disease.

Heath is wealth and health is something we all must actively protect as we live in a world that is not conducive to creating health.

We are up against growing obstacles such as increased stress, sedentary lifestyle, increasing diseases and symptoms, and toxins all around us.

Our conventional medical system treats disease.  This is a problem because we now know that most diseases can be prevented.  Key is to stay proactive in creating your health.

Interested in a personalized Alkaline Functional Plan?  Call us today at 678-335-5566  or e-mail us at [email protected] for a consultation. We have telemedicine consults and in person programs to suit your needs.

If you enjoyed this blog, please subscribe to our newsletter at alkalinewellness.com and lupusrebel.wpengine.com, and subscribe to our podcast and our Youtube channel.  Also like us on Facebook, Alkaline Health and Lupus Rebel.  We’d love to hear from you, so please comment below.

We’ve got much more to share, so stay tuned for next week’s Alkaline health blog.


The American Journal of Clinical Nutrition, Volume 104, Issue 2, 1 August 2016, Pages 324–333,https://doi.org/10.3945/ajcn.116.133561




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